Rhodovulum imhoffii (DSM 18064, CIP 109541, JCM 13589)

Name: Rhodovulum imhoffii (DSM 18064, CIP 109541, JCM 13589)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13748

Type strain

Strain Designation JA125

Culture col. no. DSM 18064 CIP 109541 JCM 13589 JA125

NCBI tax ID(s) 365340

Special Collections DSMZ JCM CIP Literature strains

Links

Rhodovulum imhoffii JA125 is an anaerobe, Gram-negative, rod-shaped prokaryote that was isolated from marine aquaculture pond.

Gram-negative rod-shaped anaerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 297330

DSM 18064,JCM 13589

@ref 20215

Last LPSN update 2025-12-16 09:50:10

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Rhodovulum

Species Rhodovulum imhoffii

Full scientific name Rhodovulum imhoffii Srinivas et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31834	negative	1 µm	0.5 µm	rod-shaped
125439	negative				97.7
125438	negative				96.494

Pigmentation

31834

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
31834	positive	growth	20-35
31834	positive	optimum	28	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
31834	positive	optimum	7.5
31834	positive	growth	06-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
7357	anaerobe
31834	facultative anaerobe

Spore formation

@ref	Spore formation	Confidence
31834
125439		94.9
125438		90.866

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31834	NaCl	positive	growth	0.5-7 %
31834	NaCl	positive	optimum	2.25 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31834	30089 ChEBI	acetate	+	carbon source
31834	35391 ChEBI	aspartate	+	carbon source
31834	29987 ChEBI	glutamate	+	carbon source
31834	17754 ChEBI	glycerol	+	carbon source
31834	25115 ChEBI	malate	+	carbon source
31834	15361 ChEBI	pyruvate	+	carbon source
31834	30031 ChEBI	succinate	+	carbon source
31834	16199 ChEBI	urea	+	carbon source

Enzymes

@ref	Value	Activity	Ec
31834	urease	+	3.5.1.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	formaldehyde oxidation	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	octane oxidation	100	3 of 3
66794	valine metabolism	100	9 of 9
66794	hydrogen production	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	butanoate fermentation	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	photosynthesis	92.86	13 of 14
66794	threonine metabolism	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	ketogluconate metabolism	87.5	7 of 8
66794	propanol degradation	85.71	6 of 7
66794	vitamin B12 metabolism	85.29	29 of 34
66794	leucine metabolism	84.62	11 of 13
66794	vitamin B1 metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	alanine metabolism	82.76	24 of 29
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	proline metabolism	81.82	9 of 11
66794	purine metabolism	80.85	76 of 94
66794	peptidoglycan biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	pyrimidine metabolism	80	36 of 45
66794	citric acid cycle	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	vitamin B6 metabolism	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	heme metabolism	71.43	10 of 14
66794	glutathione metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	methionine metabolism	69.23	18 of 26
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	cyanate degradation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	oxidative phosphorylation	62.64	57 of 91
66794	degradation of sugar alcohols	62.5	10 of 16
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	non-pathway related	60.53	23 of 38
66794	tryptophan metabolism	60.53	23 of 38
66794	elloramycin biosynthesis	60	3 of 5
66794	lipid metabolism	58.06	18 of 31
66794	degradation of pentoses	57.14	16 of 28
66794	tyrosine metabolism	57.14	8 of 14
66794	cysteine metabolism	55.56	10 of 18
66794	4-hydroxymandelate degradation	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	lysine metabolism	54.76	23 of 42
66794	urea cycle	53.85	7 of 13
66794	kanosamine biosynthesis II	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	myo-inositol biosynthesis	50	5 of 10
66794	glycine metabolism	50	5 of 10
66794	ribulose monophosphate pathway	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	sulfopterin metabolism	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	degradation of hexoses	50	9 of 18
66794	chlorophyll metabolism	50	9 of 18
66794	glycogen biosynthesis	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	ethanol fermentation	50	1 of 2
66794	arginine metabolism	50	12 of 24
66794	biotin biosynthesis	50	2 of 4
66794	degradation of sugar acids	48	12 of 25
66794	sulfate reduction	46.15	6 of 13
66794	nitrate assimilation	44.44	4 of 9
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	phenol degradation	40	8 of 20
66794	3-phenylpropionate degradation	40	6 of 15
66794	factor 420 biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	creatinine degradation	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	carnitine metabolism	37.5	3 of 8
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	arachidonic acid metabolism	33.33	6 of 18
66794	pantothenate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	d-xylose degradation	27.27	3 of 11
66794	alginate biosynthesis	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	toluene degradation	25	1 of 4
66794	allantoin degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Aquaculture
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Pond (small)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7357	marine aquaculture pond	Bhimunipatnam	India	IND	Asia
67770	Marine aquaculture pond

Taxonmaps

69479

Global distribution of 16S sequence AM180953 (>99% sequence identity) for Rhodovulum imhoffii subclade from Microbeatlas

Aquatic Samples	261
Soil Samples	79
Animal Samples	55
Plant Samples	23
Total Samples	418

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7357	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM304654v1 assembly for Rhodovulum imhoffii DSM 18064	scaffold	GCA_003046545	365340.4	2734482186	365340	67.36
66792	ASM1665330v1 assembly for Rhodovulum imhoffii DSM 18064	scaffold	GCA_016653305	365340.5	8066756896	365340	64.55

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7357	Rhodovulum imhoffii 16S rRNA gene, type strain JA125	AM180953	1398		365340

GC content

@ref	GC-content (mol%)	Method
7357	58	high performance liquid chromatography (HPLC)
31834	58

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhodovulum imhoffii DSM 18064
NCBI: GCA_003046545

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.90	no
125439	motility	BacteriaNetⓘ	yes	73.40	no
125439	gram_stain	BacteriaNetⓘ	negative	97.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	88.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodovulum imhoffii DSM 18064
NCBI: GCA_003046545.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.49	no
125438	anaerobic	anaerobicⓘ	no	70.76	no
125438	aerobic	aerobicⓘ	no	50.28	yes
125438	spore-forming	spore-formingⓘ	no	90.87	no
125438	thermophilic	thermophileⓘ	no	90.99	yes
125438	flagellated	motile2+ⓘ	yes	62.17	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Osmotic Adaptation and Compatible Solute Biosynthesis of Phototrophic Bacteria as Revealed from Genome Analyses.	Imhoff JF, Rahn T, Kunzel S, Keller A, Neulinger SC.	Microorganisms	10.3390/microorganisms9010046	2020
	Autotrophic bacterial production of polyhydroxyalkanoates using carbon dioxide as a sustainable carbon source.	Sathiyanarayanan G, Esteves S.	Front Bioeng Biotechnol	10.3389/fbioe.2025.1545438	2025
Phylogeny	Rhodovulum imhoffii sp. nov.	Srinivas TNR, Kumar PA, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.64470-0	2007

References

#7357	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18064
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#31834	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28100 (see below)
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Rate our new design

Content

About us

Rhodovulum imhoffii (DSM 18064, CIP 109541, JCM 13589)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003046545

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media